Green Eyes and Bow Ties
by Brittany Lyle
Summary: A girl with a fob watch, a madman with a blue box. 4 hearts. The boy and girl who waited. And a man who can't die. This is their story. Characters- OC, 11th Doctor, Amy, Rory, Captain Jack Harkness Pairings- 11/OC, Amy/Rory
1. Chapter 1

Thanks for checking out my story! Just want to give you all a proper warning, updates will be slow. I start college soon so I don't know how much time I will have to write.

"Right, so, where to now Pond? Ancient Greece? Ooh! How about we go to the premier of Singing in the Rain. I love that movie! They're singing, in the rain! And they dance!" the Doctor said as he ran around the control room of the TARDIS.

*RING-RING*

"Hello." Amy said when she picked up the phone

"Well, hello there. Can I speak to the Doctor?" the man asked flirtatiously.

"Who's calling?"

"Captain Jack Harkness."

Amy held her hand over the mouthpiece, "Doctor, a Captain Jack Harkness wants to talk to you."

"Oh, lovely!" the Doctor said joyfully as he took the phone from Amy. "Captain Jack! How are you? How's Torchwood? How's Alonso?"

"Look, this is important. Today, Torchwood took down an alien run orphanage, as we were removing the children we found something I think you might find interesting." Jack stated skipping over the pleasantries.

"Oh, and what might that be?"

"A girl."

"Look Jack. I'm not interested in love or a one night stand. I'm perfectly content."

"She has a fob watch."

"What was that? Did you say fob watch? Are you sure?"

"Positive. It's the 23rd of July 2012. The time is 9:30pm"

The Doctor was shocked. The possibility that there was someone else out there was shocking to say the least. "Right. Um, we're on our way." The Doctor hung up the phone and began scurrying about the control room typing in coordinates and turning off those bloody blue boring-ers that River turned on again.

"So Doctor, who's Captain Jack Harkness? Sounds handsome. Are you two... you know... together?" Amy asked as she followed him around the control panel.

"No. He's an old friend. He runs a facility in Cardiff called Torchwood. They deal with alien stuffs." The Doctor replied hastily as he yanked the control lever back and they were off, flying to Torchwood.

-INSIDE TORCHWOOD-

"Gwen move that table we don't want to lose that! Owen, Ianto get that couch out of the way. Most likely that's where he'll park it so I want to give him some space." Jack said as he put his phone is his pocket and grabbed the locator sensor he bought on the alien black market 10 years ago. As soon as everything was moved he turned the sensor on and set it in the middle of the alcove.

"What now?" Gwen asked as she stood beside Jack "Who's coming and what is he parking?"

"The Doctor. He's coming to see the girl." Jack replied. Suddenly he heard the sound of the TARDIS. "Stand back! I don't know how good of a driver his current regeneration is." The TARDIS appeared in the right middle of the alcove. Jack immediately ran to the blue wooden doors and burst into the control room. "Doctor! You've redecorated, very cool! Love the bow tie!" He walked up to the Doctor and hugged him. He turned to Amy "Well, hello there! Captain Jack Harkness, at your service." he said as he walked up to Amy and kissed her hand with a bow.

"Oy! That's my wife!" Rory exclaimed as he walked into the room.

"Goodness Jack! Always with the flirting! Give it a rest! Introductions! The boy is Rory the Roman. And the lovely lady is Amelia Pond. You two, the incorrigible flirt is Captain Jack Harkness. Now, down to business. Where is she? Let me see this fob watch." The Doctor said as walked past the trio and out the doors of the TARDIS.

"Ok, follow me. We've kept her sedated since we found her. From what we can tell, they locked her up and threw away the key. Files say that the girl, Sophia, was found as a child with the fob watch." Jack explained as he led the Doctor through Torchwood to the infirmary. "Here we are. Fob watch is on the table by the bed." Jack turned and shouted up the stairs "Owen! Let's get her out of sedation." the Doctor walked over to the bed and looked at the young woman. She had long brown hair, tan skin, and full pink lips. He turned to see a gold fob watch sitting on a tray by the bed. He picked up the fob watch and held it up to his ear. Nothing.

"Doctor, what is it?" Amy said walking up beside the Doctor.

"You two come with me. The Doctor needs to do this alone. I'll explain everything." Jack said as he left the room with the Ponds on his tail.

-Doctor's POV-

Well, this is an interesting turn of events! Never thought I would see one of these again.

"Where am I" mumbled the girl in the bed. She had the most beautiful green eyes.

"Hello! My name's the Doctor. What's your name?"

"Where am I?"

"You're at a special facility called Torchwood. The orphanage you were in was run by some very bad things. Torchwood took care of them and brought you here."

"Oh. Who are you? Where is this Torchwood place at?"

"Well, I'm the Doctor. And Torchwood is in Cardiff."

"I'm Sophia. Is that my lucky watch?"

"Yes. It's a very special fob watch. Have you ever opened it?" I asked as I handed the watch to her.

"No. Why would I? It's broken."

"How do you know its broken if you've never opened it? Well, I will go let them know you're awake. I'm sure they have som questions to ask you." I turned to leave the room.

"Doctor?"

"Yes."

"Nice bow tie."

"Well, thank you. I think bow ties are cool!" as I walked up the stairs, I heard her giggle. For some reason, it made my hearts skip a beat.

-Sophia's POV-

What was that? Did I just giggle? I don't giggle. I turned the watch over in my hand. Why did he want to know if I had ever opened the fob watch?

'Listen, you have to open the watch! Open it!' I heard a voice in my head

I pressed the button and the watch opened. I felt a light on my face and a heat in my chest as I realized one thing. I am a Time Lady. Then the pain started. So, I started screaming.


	2. Chapter 2

**Wow! I never could have expected all the support from you guys! I love you all! Here is a baby chapter. Thanks for all your patience and enjoy!**

**Brittany.**

"We need to get her on to the TARDIS now! She needs to be near time energy or else the screaming is gonna get a lot worse!" The Doctor said as he picked up the screaming Sophia. "It's gonna be ok."

"God! Why does it hurt so much?" she said as she grabbed on to his jacket.

"Well, you're changing into a Time Lady without time energy. Basically, you're growing a second heart while your brain is changing to accommodate the plethora of new information. You know when you cut off all your hair and it grows back?"

"Yeah."

"Well, it's nothing like that."

"Fan-freaking-tastic! Ugh!" she ended with a scream. The Doctor started running faster with Jack on his heels. He reached the TARDIS and ran in and set her on the floor.

"Ok, should stop hurting so much. Give it a moment." he sat beside her and held her hand while brushing her hair off her face. She stopped screaming and her eyes opened wide as her mouth opened and a puff of golden time energy blew out.

"Wow. Two hearts, that's weird, gonna have to get used to that." Sophia chuckled as she sat up. "Doctor? Why are you crying?"

"I'm not alone anymore." he whispered as he pulled her into a tight hug. She squeezed back and they sat there while the Doctor cried. She placed her hands on his head and sent him thoughts of peace making him cry harder.

"You're not alone, not anymore." She said as she kissed the top of his head.


	3. Chapter 3

-Jack's POV-

I quietly walked out of the TARDIS giving the Doctor and Sophia some privacy. I shut the door and turned to be met by the Doctor's companions Amy and Rory.

"Is the Doctor in there? Why was that girl screaming?" Amy asked

"What has the Doctor told you about Time Lords? Do you know about the Chameleon Circuit?"

"What's a Chameleon Circuit?" Rory asked

"Great!" I exclaimed as I brushed past them to walk to my office. "Come Along Ponds! Hmm, that's catchy. I should tell that one to the Doctor. Anyways, Time Lords were very tricky beings. They made themselves several backdoors just in case. I only know of three. One of which I won't go into, it involves having a spare body part lying around, its a very complicated story that's best for another day. First there's Regeneration, which I'm sure you know about. Second, the one I won't go into. And Third, the Chameleon Circuit. What the CC does is it rewrites a Time Lords DNA into Human DNA. Completely removing every bit of Time Lord from them, even their memories, and the Time Lord part of them is put into a fob watch. That's what happened to Sophia. Most likely, she was born during the Time War so to save her she was made human soon after birth. Which I think is very cruel because Martha and the Doctor said its a very painful process. So, when Sophia opened the fob watch, it was a VERY painful thing. Her DNA was being re-written back to Time Lord without being near Time Energy."

"Uh‚ Ok. That's complicated. I think I understand." Amy said as she sat down on the couch in my office.

"Yeah! If you ever want to be really confused, ask me about the second backdoor. That one will throw you for a loop! Feel free to make yourself comfortable. I have a feeling that those two are gonna be in the TARDIS awhile."

-Inside the TARDIS-

-Doctor's POV-

I slowly opened my eyes and leaned back. I looked at what I had just been laying on to see Sophia smiling at me.

"Hey! Your awake. How are you feeling?" She asked as she placed her hand over my hearts one at a time. "They seem to be working right. That's good. Do you want me to run a MedScan?"

"No. I'm fine."

"I'm gonna go find some real clothes." She said as she got up, "You sure your ok? You got this odd look on your face."

"Oh yeah! I'm fine. Wardrobe's that way."

"I know!" She tossed over her shoulder as she walked out of the control room.

'So this is really happening. I'm not alone any more.' I thought to myself as I tried to wrap my head around the fact that I'm not the last Time Lord anymore."Well, this is Wibbly-Wobbly Spacey-Wacey!"

-Sophia's POV-

"What to wear. What to wear." I flipped through the endless supply of clothes in the TARDIS wardrobe. Slowly I decided on a pair of trainers, a purple v-neck t-shirt, a white tank-top, some leather skinny jeans, and a burgundy hooded pea coat. "I think this will work." I said as I examined myself in the full-length mirror. I turned and headed back towards the control room.

"Well, this is Wibbly-Wobbly Spacey-Wacey!" the Doctor muttered to himself

"What's Spacey-Wacey?" I asked

"Oh, nothing."

"Doctor."

"What?" he turned to look at me "Well... look at you! You look..."

"Look what?"

"Um... Nice?"

"Thanks. You absolutely sure you're ok?"

"Yep! Let's go so I can properly introduce you to the gang. Well, not really a gang. Never really had a gang before until recently... Wait, no. I had a gang once before. My last regeneration had a nice big gang. We had just stopped Davros and we were flying planet Earth back"

"Doctor! You're rambling."

"Oh, sorry. Let's go." we started walking towards the door when we heard a ding from the console. "What could that be?"

"I don't know."

"Let's find out." He said with a grin. We turned back to the console and saw something sticking out of the console. "Oh, you brilliant sexy thing you!" He said as he patted the console. "She made you a sonic screwdriver!" he pulled it out of the console. "Looks just like mine. How we gonna tell them apart?" he scanned the air with the sonic. "Ooh! You got a purple one! Mine's green." He tossed the screwdriver to me, I looked it over and put it in my pocket.

"Well, lets meet this gang of yours!" we walked out of the TARDIS and into Torchwood. 


	4. Chapter 4

Hey Guys! I know it's been a while! This chapter is a little shorter than I would like, but I want to keep it separate from what's happening next. I threw a little curve ball in, mainly to challenge myself, so let me know what you think. Next chapter will either be a flashback to Sophia's time without the Doctor (to explain the curveball) or their first adventure. Please leave a comment letting me know what you think, they make me so happy when I read them! Especially Superdani's comment from chapter 2, that made me so happy! Anyways, love ya!

Enjoy!

It had been a few months since I had last seen the Doctor. He stayed about a week, then he and his companions left. He wrote me a letter. Saying that he wanted to keep me safe, but I wish he would have told me face to face.

I knew he was ok though. I could tell through the mind link we shared that he was out traveling the galaxy. I wish I could go with him...

Jack helped me get a flat in London. He visits when he can, I made sure he knows that he's always welcome and if he ever need anything he just has to call.

I was eating some Thai takeaway and watching the telly when there was a knock at my door. I grabbed my sonic screwdriver and unlocked the door from my seat on the couch.

"Come in!" I shouted "There's some extra takeaway in the kitchen Jack if you want it."

"Sophia?" A male voice asked

"Doctor? Oh my God!" I ran over and hugged him

"Sophia." He said with a hint of sadness as he hugged me back.

"What's wrong?" I asked as I led him over to the couch. He explained what happened with Amy and Rory very slowly. When he finished, a tear slipped down his cheek. "Oh, Doctor. I'm sorry. I'm so so sorry."

He ended up staying for over a week. He never left my flat, just kept re-reading the same book over and over. One night I stole it from him while he was asleep. It was the book he told me about. The one that told the story of what happened in New York. I silently set the book beside him and left the flat in search of the TARDIS. He had parked her in the alley behind my building. I used my sonic to unlock the doors and went inside to think.

"Hello Girl. What are we gonna do about him? He's been in my flat over a week, hardly moves, he just sits there on my sofa and reads that book." I said as I walked to the console. "Do you think that will work? Just forcing him into an adventure?"

The TARDIS hummed positively.

"Well, it's worth a try. I'll bring him down in the morning. Try to find something not too dangerous, ok?" I replied as I walked back out into the alley and pulled my cell phone out of my pocket to give Jack a call.

"Hey babe! What's up?" Jack said as he answered the phone

"Um, he's back. Just showed up little over a week ago and has not moved from his spot on the couch. I think he's permanently attached to it." I ended with a chuckle

"Why is the Doc sulking? Did the red-head hide his fez?"

"No, something happened to them. Have you heard of the weeping angles?"

"They're real? I thought they were a story that was told to keep little kids out of trouble?"

"Amy and Rory were sent back and the Doctor can't do anything to save them. They are really gone."

"Wow. No wonder he's depressed. What are you gonna do?"

"You want to go on an adventure?"

"I'm on my way!"

"Jack! We're not gonna leave till tomorrow!"

"That's even better!" he said suggestively

"JACK! Not while he's here! He's depressed enough as it is. I'm not even sure how I'm gonna tell him. Hell, I just might not tell him."

"You sure?"

"Yeah. We're gonna have to be careful though. You better not blow it!"

"Why would I blow it? You're gonna have to keep your hands to yourself! Why don't you want him to know anyway? It's not like you two had a thing before he left you behind."

"Look, you know why he did that! He was trying to protect me, albeit was a stupid and childish way, but that's not the point. It's just us. The last two Time Lords on existence. If I had been in his place for all those years and then all of a sudden, I'm not alone anymore! I would probably have some strong feelings."

"Yeah, I see your point. I won't do anything. By the way, who came up with the adventure idea?"

"The TARDIS. She's looking for something that's not too dangerous."

"I might have to giver her a few ideas when I get there!"

"Jack, we're not gonna take him to a pleasure planet!"

"Who said anything about him! I say we leave him behind, take the TARDIS, and have a little adventure of our own. We can be back before he even knows we're gone."

"Goodbye Jack!"

"Yeah, love you too!" he said before he hung up the phone.

"Wait, what?" Did he just say he loved me? What is going on? First the Doctor shows up, then Jack says he loves me! What am I going to do?


End file.
